grover::listFiles, are sorted client-side.grover::runInfo is ordered by .RAW file name.grover::convertDirectory returns the file paths of the converted .mzML files for all the of the raw files in the specified directory.Added the exclude argument to grover::convertDirectory and grover::runInfo to exclude raw files matching the specified patterns.
grover::runInfo now collates the sample information client-side and so the time_out argument has been removed.
The grover::groverAPI log_dir and temp_dir argument directories are now created recursively if they do not already exist.
Improved the naming of the grover::groverAPI log files to include the current system date.
The grover::groverAPI log_dir and temp_dir argument directories are now created if they do not already exist.
The grover::groverAPI temp_dir argument default is now tempdir().
grover::extant now returns TRUE if the specified API is accessible and FALSE if not.
The argument overwrite has now been added to grover::convertFile and grover::convertDirectory to enable the overwriting of local mzML files with the same file name as the raw files to be converted.
Removed the build_vignettes argument from the installation instructions in the package README as the package documetation is available online from https://jasenfinch.github.io/grover.
Removed the Introduction vignette as the majority of this information was duplicated in the package README.
rawrr](https://bioconductor.org/packages/release/bioc/html/rawrr.html) as a bioc remote to ensure the package can be installed correctly using [pak](https://pak.r-lib.org/) and [renv`.Added biocViews field to the DESCRIPTION to ensure the `rawrr Bioconductor dependency is installed automatically.
Fixed grover::converFile error when more than two options are supplied to the args parameter.
grover::converFile creates the output directory if it doesn't already exist.
Converted files now correctly zipped by grover::converFile to ensure they are readable by the mzR package.
File conversion methods grover::converFile and grover::convertDirectory now return the file path of the converted file.
Zipping of converted files for reduced storage requirements can now be specified using the zip argument and is now the default of the conversion methods such as grover::converFile.
Added grover::version to query the version number of a grover API.
grover::groverAPI now ensures that the specified temp_dir is created if not already extant.
grover::conversionArgsPeakPick fix to ensure conversion argument is correctly passed to msconverteR.rawR dependency updated to rawrr with package name change.
Fixed typo grover::runInfo console message.
Request timeout limit can now be set for grover::runInfo.
Fixed grover::runInfo when attempting to retrieve file meta-information for a corrupt .raw file.
temp_dir argument added to grover::groverAPI to enable specification of a temporary directory for converted data storage.
Fixed typo in grover::convertDirectory console message.
Added a NEWS.md file to track changes to the package.
Fixed conversion argument helpers to work correctly with msconverteR.
Converted files now returned correctly by the API.